Under the STAR-salmon directory in nf-core/rnaseq output, there is a featureCounts directory. These files are per-sample files and also have gene abundance information. e,g, https://www.synapse.org/#!Synapse:syn38868256
I recently shared the data with someone who requested the featureCounts instead of the Salmon output, because they preferred to use that for differential expression. So, we should add these files to the annotation utils if people are likely to use them.
Under the STAR-salmon directory in nf-core/rnaseq output, there is a featureCounts directory. These files are per-sample files and also have gene abundance information. e,g, https://www.synapse.org/#!Synapse:syn38868256
I recently shared the data with someone who requested the featureCounts instead of the Salmon output, because they preferred to use that for differential expression. So, we should add these files to the annotation utils if people are likely to use them.